Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/structure/Transcript.py @ 46:169d364ddd91
Uploaded
| author | m-zytnicki |
|---|---|
| date | Mon, 30 Sep 2013 03:19:26 -0400 |
| parents | 44d5973c188c |
| children |
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| 45:e454402ba9d9 | 46:169d364ddd91 |
|---|---|
| 345 newTranscript.setEnd(newEnd) | 345 newTranscript.setEnd(newEnd) |
| 346 newTranscript.setStart(newStart) | 346 newTranscript.setStart(newStart) |
| 347 newTranscript.exons = theseExons | 347 newTranscript.exons = theseExons |
| 348 return newTranscript | 348 return newTranscript |
| 349 | 349 |
| 350 | |
| 351 def getIntersection(self, transcript): | |
| 352 """ | |
| 353 Get the intersection between this transcript and another one | |
| 354 @param transcript: object to be compared to | |
| 355 @type transcript: class L{Transcript<Transcript>} | |
| 356 @return: an other transcript | |
| 357 """ | |
| 358 if self.getChromosome() != transcript.getChromosome() or self.getDirection() != transcript.getDirection(): | |
| 359 return None | |
| 360 newTranscript = Transcript() | |
| 361 newTranscript.setDirection(self.getDirection()) | |
| 362 newTranscript.setChromosome(self.getChromosome()) | |
| 363 newTranscript.setName("%s_intersect_%s" % (self.getName(), transcript.getName())) | |
| 364 newExons = [] | |
| 365 for thisExon in self.getExons(): | |
| 366 for thatExon in transcript.getExons(): | |
| 367 newExon = thisExon.getIntersection(thatExon) | |
| 368 if newExon != None: | |
| 369 newExons.append(newExon) | |
| 370 if not newExons: | |
| 371 return None | |
| 372 newTranscript.exons = newExons | |
| 373 return newTranscript | |
| 374 | |
| 375 | 350 |
| 376 def getSqlVariables(cls): | 351 def getSqlVariables(cls): |
| 377 """ | 352 """ |
| 378 Get the properties of the object that should be saved in a database | 353 Get the properties of the object that should be saved in a database |
| 379 """ | 354 """ |